nf-core/chipseq

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ChIP-seq peak-calling, QC and differential analysis pipeline.

Stars: 246
Forks: 184
Open beginner issues: 0
Indexed issues: 17

Dominant language: Nextflow
License: MIT
Last GitHub push: Jul 27, 2026
Latest indexed: Sep 19, 2026
Contributing guide: Contributing guide
Code of conduct: Code of conduct
Beginner labels: No beginner labels indexed
PR merge metrics: No merged PRs in 30d

Beginner friendly Everything

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17 open issues indexed

MACS3 is reporting that 100 paired reads are needed, even when single end data is used as input Open

bug

Difficulty 3/5 1-2 days Newbie friendliness 48/100

nf-core/chipseq#524 · 2 comments · Opened Jul 9, 2026
Change simple fasq_align_{aligner} subworkflows to fastq_align_dna Open

Difficulty 4/5 3-5 days Newbie friendliness 35/100

nf-core/chipseq#511 · Opened Apr 30, 2026
Switch local/module GTF2BED to nf-core/module BEDOPS_GTF2BED Open

enhancement

Difficulty 3/5 1-2 days Newbie friendliness 48/100

nf-core/chipseq#494 · Opened Mar 20, 2026
Clarify genome size error and update usage documentation Open

bug

Difficulty 3/5 1-2 days Newbie friendliness 45/100

nf-core/chipseq#478 · Opened Nov 4, 2025
Port bedtools_genomecov from local to nf-core module Open

enhancement improve-behaviour

Difficulty 4/5 3-5 days Newbie friendliness 38/100

nf-core/chipseq#469 · Opened Jun 24, 2025
Add minimum_alignment_q_score parameter for MAPQ filtering (similar to nf-core/cutandrun) Open

enhancement

Difficulty 4/5 3-5 days Newbie friendliness 42/100

nf-core/chipseq#463 · 2 reactions · Opened May 16, 2025
JSON schema: Chipseq Open

docs

nf-core/chipseq#458 · 1 assignee · Opened Mar 25, 2025
Enable the use of CSI bam index Open

enhancement

Difficulty 3/5 1-2 days Newbie friendliness 25/100

nf-core/chipseq#454 · 2 comments · Opened Mar 12, 2025
Output .bed file not found in the MACS2 folder Open

enhancement

Difficulty 4/5 3-5 days Newbie friendliness 25/100

nf-core/chipseq#448 · 1 comment · Opened Feb 3, 2025
Adjust x-axis to start at 1 for custom phantompeakqualtools NSC plot Open

enhancement

Difficulty 3/5 1-2 days Newbie friendliness 45/100

nf-core/chipseq#441 · Opened Dec 17, 2024
Get rid of checksamplesheet.py and switch to nf-schema Open

enhancement

Difficulty 4/5 3-5 days Newbie friendliness 25/100

nf-core/chipseq#403 · Opened Jul 19, 2024
Add --only_step options Open

enhancement

Difficulty 3/5 1-2 days Newbie friendliness 35/100

nf-core/chipseq#337 · 1 reaction · Opened Mar 8, 2023
Spike ins normalization Open

enhancement

Difficulty 5/5 Over a week Newbie friendliness 20/100

nf-core/chipseq#321 · 13 comments · 4 reactions · Opened Oct 28, 2022
Find test dataset where PRESEQ doesn't fail Open

enhancement

nf-core/chipseq#276 · 2 comments · 1 assignee · Opened May 9, 2022
Output bigwigs with macs2 p-value signal for every base-pair Open

enhancement feature-request

Difficulty 4/5 3-5 days Newbie friendliness 35/100

nf-core/chipseq#251 · 4 comments · Opened Feb 3, 2022
Merged biological replicates Open

enhancement

Difficulty 5/5 Over a week Newbie friendliness 30/100

nf-core/chipseq#213 · 4 reactions · Opened May 3, 2021
Add IDR analysis Open

enhancement feature-request

Difficulty 5/5 Over a week Newbie friendliness 25/100

nf-core/chipseq#87 · 5 comments · Opened May 30, 2019

nf-core/chipseq

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